Hi mailing list,
regarding a previous issue with the v5.3.0 and the pial boundary crossing into the ventricles (below), i have run the subjects in the beta version and the problem does not appear.
My question to the experts is now, considering it is not advised to switch versions in a data set, how 'bad' would it be to run 7 subjects in the beta version, and the other 190 or so in the v5.3.0 version?
It is after all a very small number of the total sample, would this be ok, or would you still advise against it?
Many thanks,
Areti
________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Smaragdi A. [A.Smaragdi@soton.ac.uk] Sent: 12 January 2016 18:27 To: Freesurfer support list Subject: Re: [Freesurfer] (no subject)
Hi Bruce,
thanks for the quick reply, I am running v5.3.0 from a Linux, but more than 2/3 through my data set so don't really want to swap to 6..
Where can I get the beta and how would it help?
Thanks,
Areti
________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: 12 January 2016 16:24 To: Freesurfer support list Subject: Re: [Freesurfer] (no subject)
what version are you running? I believe that this is a bug that has been fixed. Hopefully we will get version 6 out soon and upgrading will fix this, but you can download a beta and try to make sure if you want
cheers Bruce On Tue, 12 Jan 2016, Smaragdi A. wrote:
Hi mailing list,
I have encountered this problem in Freesurfer a number of times now and I wondered if any of you had any solutions.
It seems that sometimes after a recon-all has been run, there is a large overlap of the pial boundary and wm boundary, in the same region each time near the lateral ventricles (it can be on either hemisphere or both). I have attached a print screen of the issue, this time in the LH. As you can see, we have tried adding CPs and have also added WM, but after re-running it, the problem still exists. We have also tried running the randomness, but this has had no effect.
Any suggestions as to what we could do to fix this would be great - thank you!
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Areti
at the moment there is no official beta for V6, since we effectively recalled it. It will induce differences and variance into your study. An alternative would be to just rerun all of your subjects (preserving all manual edits) in V6 when it is finally out. Otherwise you will need to make sure that these subjects are balanced in your study (i.e. that they are not all controls or patients or whatever)
cheers Bruce
On Thu, 10 Mar 2016, Smaragdi A. wrote:
Hi mailing list,
regarding a previous issue with the v5.3.0 and the pial boundary crossing into the ventricles (below), i have run the subjects in the beta version and the problem does not appear.
My question to the experts is now, considering it is not advised to switch versions in a data set, how 'bad' would it be to run 7 subjects in the beta version, and the other 190 or so in the v5.3.0 version?
It is after all a very small number of the total sample, would this be ok, or would you still advise against it?
Many thanks,
Areti
From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Smaragdi A. [A.Smaragdi@soton.ac.uk] Sent: 12 January 2016 18:27 To: Freesurfer support list Subject: Re: [Freesurfer] (no subject)
Hi Bruce,
thanks for the quick reply, I am running v5.3.0 from a Linux, but more than 2/3 through my data set so don't really want to swap to 6..
Where can I get the beta and how would it help?
Thanks,
Areti
From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: 12 January 2016 16:24 To: Freesurfer support list Subject: Re: [Freesurfer] (no subject)
what version are you running? I believe that this is a bug that has been fixed. Hopefully we will get version 6 out soon and upgrading will fix this, but you can download a beta and try to make sure if you want
cheers Bruce On Tue, 12 Jan 2016, Smaragdi A. wrote:
Hi mailing list,
I have encountered this problem in Freesurfer a number of times now and I wondered if any of you had any solutions.
It seems that sometimes after a recon-all has been run, there is a large overlap of the pial boundary and wm boundary, in the same region each time near the lateral ventricles (it can be on either hemisphere or both). I have attached a print screen of the issue, this time in the LH. As you can see, we have tried adding CPs and have also added WM, but after re-running it, the problem still exists. We have also tried running the randomness, but this has had no effect.
Any suggestions as to what we could do to fix this would be great - thank you!
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Bruce,
The subject are mixed, about two from each group of four.
Would you be able to tell me when the V6 will be available? I am hoping to finish this analysis within the next couple of months and am reluctant to wait very long or to exclude these subjects..
Thanks for your help,
Areti ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: 10 March 2016 14:16 To: Freesurfer support list Subject: Re: [Freesurfer] v5.3.0 pial crossing into ventricals
Hi Areti
at the moment there is no official beta for V6, since we effectively recalled it. It will induce differences and variance into your study. An alternative would be to just rerun all of your subjects (preserving all manual edits) in V6 when it is finally out. Otherwise you will need to make sure that these subjects are balanced in your study (i.e. that they are not all controls or patients or whatever)
cheers Bruce
On Thu, 10 Mar 2016, Smaragdi A. wrote:
Hi mailing list,
regarding a previous issue with the v5.3.0 and the pial boundary crossing into the ventricles (below), i have run the subjects in the beta version and the problem does not appear.
My question to the experts is now, considering it is not advised to switch versions in a data set, how 'bad' would it be to run 7 subjects in the beta version, and the other 190 or so in the v5.3.0 version?
It is after all a very small number of the total sample, would this be ok, or would you still advise against it?
Many thanks,
Areti
From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Smaragdi A. [A.Smaragdi@soton.ac.uk] Sent: 12 January 2016 18:27 To: Freesurfer support list Subject: Re: [Freesurfer] (no subject)
Hi Bruce,
thanks for the quick reply, I am running v5.3.0 from a Linux, but more than 2/3 through my data set so don't really want to swap to 6..
Where can I get the beta and how would it help?
Thanks,
Areti
From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: 12 January 2016 16:24 To: Freesurfer support list Subject: Re: [Freesurfer] (no subject)
what version are you running? I believe that this is a bug that has been fixed. Hopefully we will get version 6 out soon and upgrading will fix this, but you can download a beta and try to make sure if you want
cheers Bruce On Tue, 12 Jan 2016, Smaragdi A. wrote:
Hi mailing list,
I have encountered this problem in Freesurfer a number of times now and I wondered if any of you had any solutions.
It seems that sometimes after a recon-all has been run, there is a large overlap of the pial boundary and wm boundary, in the same region each time near the lateral ventricles (it can be on either hemisphere or both). I have attached a print screen of the issue, this time in the LH. As you can see, we have tried adding CPs and have also added WM, but after re-running it, the problem still exists. We have also tried running the randomness, but this has had no effect.
Any suggestions as to what we could do to fix this would be great - thank you!
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Areti
we can't give you a date as it depends on various tests and such. We are hoping to get it out in the next month or so Bruce On Thu, 10 Mar 2016, Smaragdi A. wrote:
Hi Bruce,
The subject are mixed, about two from each group of four.
Would you be able to tell me when the V6 will be available? I am hoping to finish this analysis within the next couple of months and am reluctant to wait very long or to exclude these subjects..
Thanks for your help,
Areti ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: 10 March 2016 14:16 To: Freesurfer support list Subject: Re: [Freesurfer] v5.3.0 pial crossing into ventricals
Hi Areti
at the moment there is no official beta for V6, since we effectively recalled it. It will induce differences and variance into your study. An alternative would be to just rerun all of your subjects (preserving all manual edits) in V6 when it is finally out. Otherwise you will need to make sure that these subjects are balanced in your study (i.e. that they are not all controls or patients or whatever)
cheers Bruce
On Thu, 10 Mar 2016, Smaragdi A. wrote:
Hi mailing list,
regarding a previous issue with the v5.3.0 and the pial boundary crossing into the ventricles (below), i have run the subjects in the beta version and the problem does not appear.
My question to the experts is now, considering it is not advised to switch versions in a data set, how 'bad' would it be to run 7 subjects in the beta version, and the other 190 or so in the v5.3.0 version?
It is after all a very small number of the total sample, would this be ok, or would you still advise against it?
Many thanks,
Areti
From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Smaragdi A. [A.Smaragdi@soton.ac.uk] Sent: 12 January 2016 18:27 To: Freesurfer support list Subject: Re: [Freesurfer] (no subject)
Hi Bruce,
thanks for the quick reply, I am running v5.3.0 from a Linux, but more than 2/3 through my data set so don't really want to swap to 6..
Where can I get the beta and how would it help?
Thanks,
Areti
From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: 12 January 2016 16:24 To: Freesurfer support list Subject: Re: [Freesurfer] (no subject)
what version are you running? I believe that this is a bug that has been fixed. Hopefully we will get version 6 out soon and upgrading will fix this, but you can download a beta and try to make sure if you want
cheers Bruce On Tue, 12 Jan 2016, Smaragdi A. wrote:
Hi mailing list,
I have encountered this problem in Freesurfer a number of times now and I wondered if any of you had any solutions.
It seems that sometimes after a recon-all has been run, there is a large overlap of the pial boundary and wm boundary, in the same region each time near the lateral ventricles (it can be on either hemisphere or both). I have attached a print screen of the issue, this time in the LH. As you can see, we have tried adding CPs and have also added WM, but after re-running it, the problem still exists. We have also tried running the randomness, but this has had no effect.
Any suggestions as to what we could do to fix this would be great - thank you!
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Ok, great, thank you for the information! I will keep an eye out for the new version..
Thanks,
Areti ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: 10 March 2016 15:50 To: Freesurfer support list Subject: Re: [Freesurfer] v5.3.0 pial crossing into ventricals
Hi Areti
we can't give you a date as it depends on various tests and such. We are hoping to get it out in the next month or so Bruce On Thu, 10 Mar 2016, Smaragdi A. wrote:
Hi Bruce,
The subject are mixed, about two from each group of four.
Would you be able to tell me when the V6 will be available? I am hoping to finish this analysis within the next couple of months and am reluctant to wait very long or to exclude these subjects..
Thanks for your help,
Areti ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: 10 March 2016 14:16 To: Freesurfer support list Subject: Re: [Freesurfer] v5.3.0 pial crossing into ventricals
Hi Areti
at the moment there is no official beta for V6, since we effectively recalled it. It will induce differences and variance into your study. An alternative would be to just rerun all of your subjects (preserving all manual edits) in V6 when it is finally out. Otherwise you will need to make sure that these subjects are balanced in your study (i.e. that they are not all controls or patients or whatever)
cheers Bruce
On Thu, 10 Mar 2016, Smaragdi A. wrote:
Hi mailing list,
regarding a previous issue with the v5.3.0 and the pial boundary crossing into the ventricles (below), i have run the subjects in the beta version and the problem does not appear.
My question to the experts is now, considering it is not advised to switch versions in a data set, how 'bad' would it be to run 7 subjects in the beta version, and the other 190 or so in the v5.3.0 version?
It is after all a very small number of the total sample, would this be ok, or would you still advise against it?
Many thanks,
Areti
From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Smaragdi A. [A.Smaragdi@soton.ac.uk] Sent: 12 January 2016 18:27 To: Freesurfer support list Subject: Re: [Freesurfer] (no subject)
Hi Bruce,
thanks for the quick reply, I am running v5.3.0 from a Linux, but more than 2/3 through my data set so don't really want to swap to 6..
Where can I get the beta and how would it help?
Thanks,
Areti
From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: 12 January 2016 16:24 To: Freesurfer support list Subject: Re: [Freesurfer] (no subject)
what version are you running? I believe that this is a bug that has been fixed. Hopefully we will get version 6 out soon and upgrading will fix this, but you can download a beta and try to make sure if you want
cheers Bruce On Tue, 12 Jan 2016, Smaragdi A. wrote:
Hi mailing list,
I have encountered this problem in Freesurfer a number of times now and I wondered if any of you had any solutions.
It seems that sometimes after a recon-all has been run, there is a large overlap of the pial boundary and wm boundary, in the same region each time near the lateral ventricles (it can be on either hemisphere or both). I have attached a print screen of the issue, this time in the LH. As you can see, we have tried adding CPs and have also added WM, but after re-running it, the problem still exists. We have also tried running the randomness, but this has had no effect.
Any suggestions as to what we could do to fix this would be great - thank you!
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Smaragdi A.